Abstract Background The majority of the African population lives in rural areas where they heavily depend on crop and livestock production for their livelihoods. Given their socio-economic importance, we initiated a standardized multi-country (Benin, Burkina Faso, Ghana, Nigeria, Ethiopia Tanzania and Uganda) surveillance study to assess the current status of important tick-borne haemoparasites (TBHPs) of cattle. Methods We assessed pathogen prevalences (Anaplasma marginale, Anaplasma centrale, Babesia bigemina, Babesia bovis, Ehrlichia ruminantium, and Theileria parva) in the blood of 6447 animals spread over fourteen districts (two districts per country). In addition, we screened for intrinsic (sex, weight, body condition) and extrinsic (husbandry, tick exposure) risk factors as predictors of infections with TBHPs. Results There was a large macro-geographic variation observed in A. marginale, B. bigemina, B. bovis and E. ruminantium prevalences. Most correlated with the co-occurrence of their specific sets of vector-competent ticks. Highest numbers of infected cattle were found in Ghana and Benin, and lowest in Burkina Faso. While T. parva was seldomly found (Uganda only: 3.0%), A. marginale was found in each country with a prevalence of at least 40%. Babesia bovis infected individuals had lower body condition scores. Age (as estimated via body weight) was higher in A. marginale infected cattle, but was negatively correlated with B. bigemina and E. ruminantium prevalences. Ehrlichia ruminantium infection was more often found in males, and A. marginale more often in transhumance farming. High levels of co-infection, especially the combination A. marginale × B. bigemina, were observed in all countries, except for Uganda and Burkina Faso. Babesia bigemina was more or less often observed than expected by chance, when cattle were also co-infected with E. ruminantium or A. marginale, respectively. Conclusions Tick-borne pathogens of cattle are ubiquitous in African’s smallholder cattle production systems. Our standardized study will help a wide range of stakeholders to provide recommendations for TBHP surveillance and prevention in cattle, especially for B. bovis which heavily impacts production and continues its spread over the African continent via the invasive Rhipicephalus microplus tick. Graphical Abstract